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- PDB-2ijk: Structure of a Rom protein dimer at 1.55 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 2ijk
TitleStructure of a Rom protein dimer at 1.55 angstrom resolution
ComponentsRegulatory protein rop
KeywordsTRANSCRIPTION REGULATOR / Rom / Rop / ColE1 plasmid copy control
Function / homologyHelix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStruble, E.B.
CitationJournal: Proteins / Year: 2008
Title: New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition.
Authors: Struble, E.B. / Ladner, J.E. / Brabazon, D.M. / Marino, J.P.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein rop
B: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)14,3262
Polymers14,3262
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-29 kcal/mol
Surface area6340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.391, 39.364, 27.100
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein rop / RNA one modulator / ROM


Mass: 7162.896 Da / Num. of mol.: 2 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% ...Details: Hanging drop contained 1 uL protein/RNA mixture (0.3 0.4 mM complex) and 1 uL well buffer (50 mM sodium cacodylate pH 6.0, 0.1 M potassium chloride, 25 mM magnesium chloride, and 15% isopropanol)., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 2, 2006 / Details: Blue Max-flux confocal mirrors
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 14338 / % possible obs: 94.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.7 / Num. unique all: 913 / % possible all: 60.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASER1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ROP

1rop


Resolution: 1.55→48.91 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.494 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 729 5.1 %RANDOM
Rwork0.16942 ---
obs0.17181 13607 94.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.07 Å2
2---0.34 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 0 165 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9661237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3045113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6682552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.05158
X-RAY DIFFRACTIONr_chiral_restr0.10.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2562
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2643
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4551.5591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1052904
X-RAY DIFFRACTIONr_scbond_it3.3353362
X-RAY DIFFRACTIONr_scangle_it4.7944.5333
X-RAY DIFFRACTIONr_rigid_bond_restr1.9373953
X-RAY DIFFRACTIONr_sphericity_free4.8193165
X-RAY DIFFRACTIONr_sphericity_bonded3.2413912
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 17 -
Rwork0.368 638 -
obs--57.51 %

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